Hi,
Giovanni is right: there are no absolute rules about order or even names of manuals. Usually, Great is the first or the second manual; if it is the second, then Choir will be the first.
Historically, having Choir first comes from the baroque tradition of Rückpositiv in Germany or positif de dos in France, i.e. where the Choir division is located behind the player: in this case, it is technically much easier for the organ builder to put the Choir manual first and the Great second.
On other baroque organs (e.g. those by Silbermann), both divisions are in the same case, with Great below (and the other division is, quite appropriately, called Oberwerk). You would than have Great as first manual, and the Oberwerk second.
On some big instruments, you can also have a Brustwerk, a division located right above the manuals and at the front of the case (Brust=chest). The builder would then find it most convenient to put its manual closest to it, i.e. the last manual.
In French baroque organs, you sometimes have an Écho division, which indeed tends to be the last manual. For example, the Cliquot organ in Poitiers has the following order:
1 - Positif (Choir)
2 - Grand-Orgue (Great)
3 - Récit ("Swell", except that it's not swellable)
4 - Écho
and in the Dom Bedos organ in Bordeaux, we have:
1 - Positif
2 - Grand-Orgue
3 - Bombarde (contains strong reeds)
4 - Récit
5 - Écho
In French romantic organs, the Positif(=Choir) division is often located inside the main organ case, so there is no reason to have it as the first manual, and the most common order in a three-manual instrument is Great-Choir-Swell (with the Swell now being swellable, i.e. enclosed inside a box with shutters).
If an organ has electrical action, the builder could of course order the manuals any way he likes (rods can't be bent, but cables can!), but for convenience, most builders just stuck to the (by then well established) order of manuals that was customary in their particular country and time period - so that accounts for a great variety of possibilities, as Giovanni mentioned.
Probably the only absolute rules (i.e. with no exceptions known to me) are that Great comes before Swell and Solo, and that Choir comes before Solo.